Add support for GridType.None

src/main/java/org/embl/mobie/MoBIE.java

@@ -168,6 +168,13 @@ public MoBIE( String tablePath, List< String > imageColumns, List< String > labe
 
 		this.settings = settings;
 
+		// TODO: if the gridType is None we may want to rather use SourcesFromPathsCreator( )
+		//   where we prefetch the paths from the table based on the image type
+		//   https://github.com/mobie/mobie-viewer-fiji/issues/1151
+		//   in fact then the table layout is different as each row can have a different data type
+		//   Old table: image_path, segmentation_path (one-to-one relation of an image and a segmentation)
+		//   New Table: path, image_type (no relation of an image and a segmentation needed, could be defined by having the same view_id)
+		//   Both can be useful and I guess we should keep on supporting both
 		final SourcesFromTableCreator sourcesCreator = new SourcesFromTableCreator( tablePath, imageColumns, labelColumns, root, pathMapping, grid );
 
 		final List< ImageFileSources > imageSources = sourcesCreator.getImageSources();

src/main/java/org/embl/mobie/lib/files/FileSourcesDataSetter.java

@@ -64,7 +64,9 @@ public class FileSourcesDataSetter
 	private final List< LabelFileSources > labels;
 	private final Table regionTable;
 
-	public FileSourcesDataSetter( List< ImageFileSources > images, List< LabelFileSources > labels, Table regionTable )
+	public FileSourcesDataSetter( List< ImageFileSources > images,
+								  List< LabelFileSources > labels,
+								  Table regionTable )
 	{
 		this.images = images;
 		this.labels = labels;
@@ -112,23 +114,86 @@ public void addDataAndDisplaysAndViews( Dataset dataset )
 			}
 		}
 
-		addGridView( dataset, allSources, regionTable );
+		// note that currently the way they are constructed
+		// all sources will have the same grid type
+		// thus it suffices to check the first one
+		// ( obviously this smells as if this logic could be improved )
+		if ( allSources.get( 0 ).getGridType().equals( GridType.None ) )
+		{
+			addIndividualViews( dataset, allSources );
+		}
+		else
+		{
+			// create a grid view for all sources
+			// assuming that they all live in the same grid
+			addGridView( dataset, allSources );
+		}
+	}
+
+	// This assumes that all the individual views are similar
+	// that are part of the same ImageFileSources, as they get the same initial metadata
+	// in terms of number of channels, timepoints and contrast limits
+	private void addIndividualViews( Dataset dataset, ArrayList< ImageFileSources > fileSourcesList )
+	{
+		for ( ImageFileSources sources : fileSourcesList )
+		{
+			for ( String source : sources.getSources() )
+			{
+				final List< Display< ? > > displays = new ArrayList<>();
+				final List< Transformation > transformations = new ArrayList<>();
+
+				if ( sources instanceof LabelFileSources )
+				{
+					// SegmentationDisplay
+					final SegmentationDisplay< AnnotatedSegment > segmentationDisplay
+							= new SegmentationDisplay<>( source, Collections.singletonList( source ) );
+					final int numLabelTables = ( ( LabelFileSources ) sources ).getNumLabelTables();
+					segmentationDisplay.setShowTable( numLabelTables > 0 );
+					displays.add( segmentationDisplay );
+				}
+				else
+				{
+					// ImageDisplay
+					final Metadata metadata = sources.getMetadata();
+					ImageDisplay< ? > imageDisplay = new ImageDisplay<>( source,
+							Collections.singletonList( source ),
+							metadata.color,
+							metadata.contrastLimits );
+					displays.add( imageDisplay );
+				}
+
+				// construct and add the view
+				//
+				final ImageZoomViewerTransform viewerTransform = new ImageZoomViewerTransform( source, 0 );
+				final View view = new View(
+						source,
+						"data",
+						displays,
+						null,
+						viewerTransform,
+						false,
+						null );
+
+				dataset.views().put( view.getName(), view );
+			}
+		}
+
 	}
 
-	private void addGridView( Dataset dataset, ArrayList< ImageFileSources > allSources, Table regionTable )
+	private void addGridView( Dataset dataset, ArrayList< ImageFileSources > fileSourcesList )
 	{
 		RegionDisplay< AnnotatedRegion > regionDisplay = null;
 		final List< Display< ? > > displays = new ArrayList<>();
 		final List< Transformation > transformations = new ArrayList<>();
 
-		for ( ImageFileSources sources : allSources )
+		for ( ImageFileSources sources : fileSourcesList )
 		{
 			List< String > sourceNames = sources.getSources();
 			final int numRegions = sourceNames.size();
 
 			if ( regionDisplay == null )
 			{
-				// init RegionDisplay
+				// init RegionDisplay for allSources, assuming that they all should live in the same grid
 				regionDisplay = new RegionDisplay<>( regionTable.name() );
 
 				// add table
@@ -170,10 +235,10 @@ private void addGridView( Dataset dataset, ArrayList< ImageFileSources > allSour
 				//System.out.println("Region: " +  regionName + "; source: " + sourceNames.get( regionIndex ) );
 			}
 
-			if ( sources.getSources().size() == 1 )
+			if ( sources.getSources().size() == 1 ) // no need to build a grid view
 			{
 				String source = sources.getSources().get( 0 );
-				// no need to build a grid view
+
 				if ( sources instanceof LabelFileSources )
 				{
 					// SegmentationDisplay
@@ -273,7 +338,7 @@ else if ( sources.getGridType().equals( GridType.Transformed ) )
 
 		// construct and add the view
 		//
-		final ImageZoomViewerTransform viewerTransform = new ImageZoomViewerTransform( allSources.get( 0 ).getSources().get( 0 ), 0 );
+		final ImageZoomViewerTransform viewerTransform = new ImageZoomViewerTransform( fileSourcesList.get( 0 ).getSources().get( 0 ), 0 );
 		final View view = new View( "all images", "data", displays, transformations, viewerTransform, false, null );
 		dataset.views().put( view.getName(), view );
 	}

src/main/java/org/embl/mobie/lib/files/ImageFileSources.java

@@ -88,6 +88,7 @@ public ImageFileSources( String name, String pathRegex, Integer channelIndex, St
 		}
 
 		// TODO: how to deal with the inconsistent metadata (e.g. number of time-points)?
+		// FIXME: We don't always want to prefetch this as this is expensive..
 		setMetadata( channelIndex );
 
 		// TODO: move this out to a separate function

src/main/java/org/embl/mobie/lib/files/SourcesFromPathsCreator.java

@@ -37,9 +37,8 @@
 
 public class SourcesFromPathsCreator
 {
-	private List< ImageFileSources > imageSources;
-	private List< LabelFileSources > labelSources;
-	private Table regionTable;
+	private final List< ImageFileSources > imageSources;
+	private final List< LabelFileSources > labelSources;
 
 	public SourcesFromPathsCreator( List < String > imagePaths, List < String > labelPaths, List < String > labelTablePaths, String root, GridType grid )
 	{

src/main/java/org/embl/mobie/lib/transform/viewer/MoBIEViewerTransformAdjuster.java

@@ -115,7 +115,8 @@ public AffineTransform3D getSingleSourceTransform()
 	}
 
 	// TODO: This does not seem to work well if one of the sources
-	//   contains a rotation: https://github.com/mobie/mobie-viewer-fiji/issues/1153
+	//   contains a rotation: https://github.com/mobie/mobie-viewer-fiji/issues/1154
+	//   For debugging this also a single source would suffice.
 	public AffineTransform3D getMultiSourceTransform() {
 		SynchronizedViewerState state = bdvHandle.getViewerPanel().state();
 		final RealInterval mask = TransformHelper.createMask( sources, state.getCurrentTimepoint() );

src/test/java/projects/OpenLocalTestTable.java

@@ -0,0 +1,51 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2024 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package projects;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.command.open.OpenTableCommand;
+import org.embl.mobie.lib.transform.GridType;
+
+import java.io.File;
+import java.io.IOException;
+
+public class OpenLocalTestTable
+{
+	public static void main( String[] args ) throws IOException
+	{
+		final ImageJ imageJ = new ImageJ();
+		imageJ.ui().showUI();
+
+		OpenTableCommand command = new OpenTableCommand();
+		command.table = new File("/Users/tischer/Desktop/mobie-table-test/table.csv");
+		command.gridType = GridType.None;
+		command.images = "Path";
+		command.run();
+	}
+}